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(CNN) - An Argentine prosecutor who accused top government officials of a cover-up in the country's deadliest terror attack was murdered, a federal judge said Tuesday.

The ruling marks the first time a judge has called the death of public prosecutor Alberto Nisman a murder, in a case that has been rife with speculation and conspiracy theories.

Nisman was found dead in his Buenos Aires apartment on January 18, 2015, from a gunshot wound to his head. Days earlier, he had filed a report accusing former President Cristina Fernández de Kirchner and other officials of covering up Iran's involvement in a 1994 Jewish community center bombing that left 85 people dead and more than 300 wounded.

Initially, Fernández and others called his death a suicide. But tests found no gunpowder residue on Nisman's hands or traces of blood on his arms to suggest the bullet wound was self-inflicted, judge Julián Ercolini wrote in a 656-page ruling.

"The death of Prosecutor Nisman was not a suicide, and was brought about by a third party and in a painful manner," Ercolini said in the ruling.

In the ruling, Ercolini charged Diego Lagomarsino with accessory to murder. Lagomarsino was the last person inside the prosecutor's apartment, and Nisman was killed with a weapon belonging to Lagomarsino, the judge said.

Lagomarsino, an IT security expert who worked for Nisman, has maintained that he gave Nisman his gun at the prosecutor's insistence. According to Lagomarsino, Nisman called him to his home on January 17 worried for his safety. But Lagomarsino has insisted he had nothing to do with Nisman's death.

When he died, Nisman was overseeing the investigation of the 1994 bombing of the Argentine Israelite Mutual Association.

In his report, Nisman alleged that Fernandez and Foreign Minister Héctor Timerman wanted to cover up Iran's involvement in order to boost trade -- specifically, oil imports and grain exports -- with the Islamic republic.

The Fernández administration hit back sharply after the allegations, denying a cover-up of Iranian links. At the time, Fernández said Nisman's claims "were intended to lie, disguise and confuse."

After filing the complaint, Nisman made a prescient comment about the investigation: "I could end up dead from this," he told a reporter.

Then, the night before he was scheduled to testify before lawmakers, his body was found.

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